The core mission of the NMP is to interpret the relationship between people, nature, and culture with an open-minded view, to show the beauty of nature, and thus help the public to have a better understanding of the relationship between humans and the natural environment, and develop the concept of natural preservation. The museum explains the importance of environmental balance and the adaptation of cultures. It thus presents different cultures developed as a result of different adaptations to different geographical topographies. The NMP also helps the public to learn to respect and appreciate different tribal cultures through displaying their diversity. In accordance with this core mission, the three major themes for the first stage exhibition of the NMP to be presented are "The Natural History of Taiwan", "The Prehistory of Taiwan" and "The Indigenous Peoples of Taiwan".

To begin with, the visitor will first arrive at The Natural History of Taiwan Exhibition Hall through the entrance of the second floor exhibition hall. The theme of this exhibition hall is the geographical and ecological changes of the land we have lived on since the birth of the earth. Then as one follows the designated route and enters the atrium, one will find him/herself in the Museum Forum in the middle of the atrium with a raised ceiling. This area makes use of multimedia facilities for illustrating different forum topics concerning the people, their ways of life and nature. The first floor in the basement area surrounding the atrium is The Prehistory of Taiwan Exhibition Hall which shows different cultures, activities and inventions developed as the results of the adaptations of prehistoric people on this land under different environmental circumstances, in different periods and locations. Finally, one can follow the route to go back to the second floor and enter The Indigenous Peoples of Taiwan Exhibition Hall which demonstrates the diverse cultures which developed as a result of adaptations of the indigenous peoples in Taiwan in different environments. This exhibition route, which shows the birth, migration, and sophisticated cultures of the Austronesian tribes, allows the visitors to gain an overview of the changes occurring throughout tens of millions of years in Taiwan, but also get a comprehensive understanding of the interaction between the people, nature and the various cultures on this island.